The mouse t-complex on chromosome 17 has long been a focus of interest for developmental biologists. Because many embryonic lethal mutations are localized in the region, corresponding genes of importance in development are inferred to reside there, and it is a prime target for high priority analysis. The findings of our collaborators that the region contains a large number of otherwise unknown genes, including many expressed selectively in the ectoplacental cone, underline the importance of the region and provided probes to screen for substrates for long-range sequence analysis. We have assembled 16.0 Mb DNA in three large contigs, representing just over 1/2 of the estimated 30Mb region. Contig 1, ~8.0 Mb, extending from MGD cM 4.0 to 8.3, with 188 BACs formatted with 166 STSs, includes markers Brachyury at the proximal end and D17Leh55 distally, and covers the distal border of inversion 2, where other sequence coverage is poor. Contig 2, 7.3 Mb, spans MGD cM 8.8 to 16.4, and consists of 177 BACs and 157 STSs. Contig 3, 1Mb proximal to H2-K, defines the recessive lethal tw5 critical region, includes 13 BACs and 19 STSs, and precisely localizes markers D17Mit147, D17Mit16, and D17Mit62. To facilitate the analysis, maps were, where possible, confirmed by fingerprinting data; and in conjunction with the mouse genome sequencing consortium efforts, 43 BACs were sequenced. We have annotated 7.97 Mb sequence that independently verifies and augments whole genome shotgun assemblies. This provides candidate genes and clones to identify various t-complex lethal mutations in conjunction with collaborating laboratories, and to investigate critical processes in early development. As a technological approach to systematic studies of many genes, we have initiated pilot screening for phage-display antibodies. A range of antibodies for a candidate gene, FANCD2 have been recovered and are being further characterized.